A shortage of mangoes in Western Australia's far north has forced Perth charities to refund hundreds of people who purchased boxes of the fruit as part of a fundraiser.

The Dogs Refuge Home and the Cat Haven have begun refunding people who pre-purchased a 10-kilogram box of mangoes for $40.

The mangoes were supposed to come directly from Kununurra growers, with part proceeds from every purchase donated to the charity.

But the fundraiser was cancelled due to a lack of available mangoes.

WA Department of Agriculture and Food industry officer Peter Johnson said it was a "strange" year for mango production.

"We've pretty much had two crops this year - there was an early one back in September, early October, and then there's going to be a bit of late fruit coming in mid-November - and not a lot in between…